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add UNITS: and DATA: metadata tags to force field files

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This commit is contained in:
Axel Kohlmeyer
2022-07-05 07:11:09 -04:00
parent f58d413fbd
commit 89e0989522
17 changed files with 245 additions and 228 deletions
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1
examples/amoeba/amoeba_ubiquitin.prm
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@ -1,3 +1,4 @@
!! DATE: 2022-07-05 UNITS: real
############################## ##############################
## ## ## ##

1
examples/amoeba/amoeba_water.prm
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@ -1,3 +1,4 @@
!! DATE: 2022-07-05 UNITS: real
############################## ##############################
## ## ## ##

1
examples/amoeba/hippo_water.prm
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@ -1,3 +1,4 @@
!! DATE: 2022-07-05 UNITS: real
############################## ##############################
## ## ## ##

33
examples/amoeba/log.5Jul22.ubiquitin.g++.1
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@ -57,10 +57,11 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors 19 = max # of 1-4 neighbors
21 = max # of special neighbors 21 = max # of special neighbors
special bonds CPU = 0.003 seconds special bonds CPU = 0.003 seconds
read_data CPU = 0.042 seconds read_data CPU = 0.077 seconds
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05
Skipping section: AMOEBA Protein Force Field Atom Classes Skipping section: AMOEBA Protein Force Field Atom Classes
Skipping section: Torsion-Torsion Parameters Skipping section: Torsion-Torsion Parameters
Skipping section: Biopolymer Atom Type Conversions Skipping section: Biopolymer Atom Type Conversions
@ -74,7 +75,7 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors 19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors 58 = max # of 1-5 neighbors
21 = max # of special neighbors 21 = max # of special neighbors
special bonds CPU = 0.004 seconds special bonds CPU = 0.005 seconds
# thermo output # thermo output
@ -123,29 +124,29 @@ Per MPI rank memory allocation (min/avg/max) = 258.3 | 258.3 | 258.3 Mbytes
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776 3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224 4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369 5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
Loop time of 6.52854 on 1 procs for 5 steps with 9737 atoms Loop time of 6.65546 on 1 procs for 5 steps with 9737 atoms
Performance: 0.066 ns/day, 362.697 hours/ns, 0.766 timesteps/s Performance: 0.065 ns/day, 369.748 hours/ns, 0.751 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown: AMOEBA timing breakdown:
Init time: 0.0100839 0.15% Init time: 0.0105468 0.16%
Hal time: 1.54573 23.70% Hal time: 1.57051 23.62%
Mpole time: 0.806911 12.37% Mpole time: 0.805631 12.12%
Induce time: 2.63878 40.46% Induce time: 2.69099 40.48%
Polar time: 1.51971 23.30% Polar time: 1.57015 23.62%
Total time: 6.52122 Total time: 6.64783
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 6.5212 | 6.5212 | 6.5212 | 0.0 | 99.89 Pair | 6.6478 | 6.6478 | 6.6478 | 0.0 | 99.89
Bond | 0.0049597 | 0.0049597 | 0.0049597 | 0.0 | 0.08 Bond | 0.0052138 | 0.0052138 | 0.0052138 | 0.0 | 0.08
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0010627 | 0.0010627 | 0.0010627 | 0.0 | 0.02 Comm | 0.0010535 | 0.0010535 | 0.0010535 | 0.0 | 0.02
Output | 0.00032106 | 0.00032106 | 0.00032106 | 0.0 | 0.00 Output | 0.00033674 | 0.00033674 | 0.00033674 | 0.0 | 0.01
Modify | 0.00083249 | 0.00083249 | 0.00083249 | 0.0 | 0.01 Modify | 0.00085639 | 0.00085639 | 0.00085639 | 0.0 | 0.01
Other | | 0.0001265 | | | 0.00 Other | | 0.000145 | | | 0.00
Nlocal: 9737 ave 9737 max 9737 min Nlocal: 9737 ave 9737 max 9737 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

33
examples/amoeba/log.5Jul22.ubiquitin.g++.4
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@ -57,10 +57,11 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors 19 = max # of 1-4 neighbors
21 = max # of special neighbors 21 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.001 seconds
read_data CPU = 0.049 seconds read_data CPU = 0.036 seconds
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05
Skipping section: AMOEBA Protein Force Field Atom Classes Skipping section: AMOEBA Protein Force Field Atom Classes
Skipping section: Torsion-Torsion Parameters Skipping section: Torsion-Torsion Parameters
Skipping section: Biopolymer Atom Type Conversions Skipping section: Biopolymer Atom Type Conversions
@ -123,29 +124,29 @@ Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776 3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224 4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369 5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
Loop time of 2.20325 on 4 procs for 5 steps with 9737 atoms Loop time of 2.1516 on 4 procs for 5 steps with 9737 atoms
Performance: 0.196 ns/day, 122.403 hours/ns, 2.269 timesteps/s Performance: 0.201 ns/day, 119.533 hours/ns, 2.324 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads 99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown: AMOEBA timing breakdown:
Init time: 0.0117181 0.53% Init time: 0.0116891 0.54%
Hal time: 0.442973 20.14% Hal time: 0.423411 19.72%
Mpole time: 0.287778 13.09% Mpole time: 0.269917 12.57%
Induce time: 0.94261 42.86% Induce time: 0.929983 43.30%
Polar time: 0.514081 23.38% Polar time: 0.512586 23.87%
Total time: 2.19916 Total time: 2.14759
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 2.1991 | 2.1992 | 2.1996 | 0.0 | 99.82 Pair | 2.1477 | 2.1477 | 2.1477 | 0.0 | 99.82
Bond | 0.0011873 | 0.0014547 | 0.0016743 | 0.5 | 0.07 Bond | 0.001184 | 0.0014529 | 0.0016771 | 0.5 | 0.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0014371 | 0.0018264 | 0.0020772 | 0.6 | 0.08 Comm | 0.0015356 | 0.0017027 | 0.001922 | 0.4 | 0.08
Output | 0.0002413 | 0.00029218 | 0.00037812 | 0.0 | 0.01 Output | 0.00027025 | 0.0003219 | 0.00040484 | 0.0 | 0.01
Modify | 0.0002694 | 0.00029873 | 0.00032365 | 0.0 | 0.01 Modify | 0.00028633 | 0.00030716 | 0.00032386 | 0.0 | 0.01
Other | | 0.000135 | | | 0.01 Other | | 0.0001328 | | | 0.01
Nlocal: 2434.25 ave 2498 max 2390 min Nlocal: 2434.25 ave 2498 max 2390 min
Histogram: 1 1 0 0 1 0 0 0 0 1 Histogram: 1 1 0 0 1 0 0 0 0 1

37
examples/amoeba/log.5Jul22.water_box.amoeba.g++.1
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@ -40,13 +40,14 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000 seconds special bonds CPU = 0.001 seconds
read_data CPU = 0.004 seconds read_data CPU = 0.012 seconds
# force field # force field
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key pair_coeff * * amoeba_water.prm amoeba_water_box.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -57,7 +58,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors 2 = max # of 1-5 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000 seconds special bonds CPU = 0.001 seconds
# thermo output # thermo output
@ -111,29 +112,29 @@ Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 Mbytes
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412 80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604 90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924 100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
Loop time of 9.20176 on 1 procs for 100 steps with 648 atoms Loop time of 9.23157 on 1 procs for 100 steps with 648 atoms
Performance: 0.939 ns/day, 25.560 hours/ns, 10.867 timesteps/s Performance: 0.936 ns/day, 25.643 hours/ns, 10.832 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown: AMOEBA timing breakdown:
Init time: 0.0197604 0.22% Init time: 0.0194993 0.21%
Hal time: 0.384028 4.18% Hal time: 0.383028 4.15%
Mpole time: 0.939829 10.23% Mpole time: 0.935775 10.15%
Induce time: 6.03232 65.64% Induce time: 6.06306 65.76%
Polar time: 1.81401 19.74% Polar time: 1.81839 19.72%
Total time: 9.18998 Total time: 9.21978
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 9.1903 | 9.1903 | 9.1903 | 0.0 | 99.88 Pair | 9.2201 | 9.2201 | 9.2201 | 0.0 | 99.88
Bond | 0.0024644 | 0.0024644 | 0.0024644 | 0.0 | 0.03 Bond | 0.0024949 | 0.0024949 | 0.0024949 | 0.0 | 0.03
Neigh | 0.0045623 | 0.0045623 | 0.0045623 | 0.0 | 0.05 Neigh | 0.0046051 | 0.0046051 | 0.0046051 | 0.0 | 0.05
Comm | 0.0024492 | 0.0024492 | 0.0024492 | 0.0 | 0.03 Comm | 0.0023611 | 0.0023611 | 0.0023611 | 0.0 | 0.03
Output | 0.00046866 | 0.00046866 | 0.00046866 | 0.0 | 0.01 Output | 0.00045516 | 0.00045516 | 0.00045516 | 0.0 | 0.00
Modify | 0.00071308 | 0.00071308 | 0.00071308 | 0.0 | 0.01 Modify | 0.00070554 | 0.00070554 | 0.00070554 | 0.0 | 0.01
Other | | 0.000819 | | | 0.01 Other | | 0.0008327 | | | 0.01
Nlocal: 648 ave 648 max 648 min Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

33
examples/amoeba/log.5Jul22.water_box.amoeba.g++.4
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@ -41,12 +41,13 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000 seconds special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds read_data CPU = 0.005 seconds
# force field # force field
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key pair_coeff * * amoeba_water.prm amoeba_water_box.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -111,29 +112,29 @@ Per MPI rank memory allocation (min/avg/max) = 56.38 | 56.38 | 56.38 Mbytes
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412 80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604 90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924 100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
Loop time of 3.56288 on 4 procs for 100 steps with 648 atoms Loop time of 3.62992 on 4 procs for 100 steps with 648 atoms
Performance: 2.425 ns/day, 9.897 hours/ns, 28.067 timesteps/s Performance: 2.380 ns/day, 10.083 hours/ns, 27.549 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads 99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown: AMOEBA timing breakdown:
Init time: 0.0211994 0.60% Init time: 0.0211291 0.58%
Hal time: 0.112106 3.15% Hal time: 0.114718 3.17%
Mpole time: 0.321265 9.04% Mpole time: 0.329891 9.11%
Induce time: 2.48321 69.88% Induce time: 2.5339 69.99%
Polar time: 0.61587 17.33% Polar time: 0.620639 17.14%
Total time: 3.55367 Total time: 3.6203
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 3.5543 | 3.5544 | 3.5544 | 0.0 | 99.76 Pair | 3.6209 | 3.621 | 3.6211 | 0.0 | 99.75
Bond | 0.00084867 | 0.0008661 | 0.00088053 | 0.0 | 0.02 Bond | 0.00085544 | 0.00087038 | 0.00090469 | 0.0 | 0.02
Neigh | 0.0014115 | 0.0014132 | 0.0014157 | 0.0 | 0.04 Neigh | 0.0014354 | 0.0014405 | 0.0014453 | 0.0 | 0.04
Comm | 0.0044654 | 0.0045745 | 0.004671 | 0.1 | 0.13 Comm | 0.004823 | 0.0048746 | 0.0049092 | 0.0 | 0.13
Output | 0.00037263 | 0.00042347 | 0.00054242 | 0.0 | 0.01 Output | 0.00038727 | 0.00043628 | 0.00055233 | 0.0 | 0.01
Modify | 0.00035262 | 0.00036625 | 0.00037678 | 0.0 | 0.01 Modify | 0.00033814 | 0.0003491 | 0.00037267 | 0.0 | 0.01
Other | | 0.0008691 | | | 0.02 Other | | 0.0009691 | | | 0.03
Nlocal: 162 ave 164 max 159 min Nlocal: 162 ave 164 max 159 min
Histogram: 1 0 0 0 0 0 1 0 1 1 Histogram: 1 0 0 0 0 0 1 0 1 1

35
examples/amoeba/log.5Jul22.water_box.hippo.g++.1
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@ -47,6 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
pair_style hippo pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key pair_coeff * * hippo_water.prm hippo_water_box.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -108,31 +109,31 @@ Per MPI rank memory allocation (min/avg/max) = 56.46 | 56.46 | 56.46 Mbytes
3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567 3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567
4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638 4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638
5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123 5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123
Loop time of 0.328811 on 1 procs for 5 steps with 648 atoms Loop time of 0.326218 on 1 procs for 5 steps with 648 atoms
Performance: 1.314 ns/day, 18.267 hours/ns, 15.206 timesteps/s Performance: 1.324 ns/day, 18.123 hours/ns, 15.327 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
HIPPO timing breakdown: HIPPO timing breakdown:
Init time: 0.000849843 0.26% Init time: 0.000842282 0.26%
Repulse time: 0.0386964 11.79% Repulse time: 0.0383544 11.78%
Disp time: 0.0176955 5.39% Disp time: 0.0173558 5.33%
Mpole time: 0.0625716 19.06% Mpole time: 0.0613861 18.85%
Induce time: 0.122108 37.20% Induce time: 0.121337 37.26%
Polar time: 0.0762897 23.24% Polar time: 0.0763061 23.43%
Qxfer time: 0.010031 3.06% Qxfer time: 0.0101016 3.10%
Total time: 0.328242 Total time: 0.325683
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.32826 | 0.32826 | 0.32826 | 0.0 | 99.83 Pair | 0.3257 | 0.3257 | 0.3257 | 0.0 | 99.84
Bond | 0.00014786 | 0.00014786 | 0.00014786 | 0.0 | 0.04 Bond | 0.00013737 | 0.00013737 | 0.00013737 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 9.3603e-05 | 9.3603e-05 | 9.3603e-05 | 0.0 | 0.03 Comm | 0.0001122 | 0.0001122 | 0.0001122 | 0.0 | 0.03
Output | 0.00022715 | 0.00022715 | 0.00022715 | 0.0 | 0.07 Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.06
Modify | 5.5594e-05 | 5.5594e-05 | 5.5594e-05 | 0.0 | 0.02 Modify | 3.4058e-05 | 3.4058e-05 | 3.4058e-05 | 0.0 | 0.01
Other | | 2.723e-05 | | | 0.01 Other | | 2.595e-05 | | | 0.01
Nlocal: 648 ave 648 max 648 min Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

35
examples/amoeba/log.5Jul22.water_box.hippo.g++.4
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@ -47,6 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
pair_style hippo pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key pair_coeff * * hippo_water.prm hippo_water_box.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -108,31 +109,31 @@ Per MPI rank memory allocation (min/avg/max) = 55.94 | 55.94 | 55.94 Mbytes
3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567 3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567
4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638 4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638
5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123 5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123
Loop time of 0.122174 on 4 procs for 5 steps with 648 atoms Loop time of 0.122 on 4 procs for 5 steps with 648 atoms
Performance: 3.536 ns/day, 6.787 hours/ns, 40.925 timesteps/s Performance: 3.541 ns/day, 6.778 hours/ns, 40.984 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads 98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
HIPPO timing breakdown: HIPPO timing breakdown:
Init time: 0.00112002 0.93% Init time: 0.000810221 0.67%
Repulse time: 0.0120679 9.97% Repulse time: 0.0125366 10.36%
Disp time: 0.00648732 5.36% Disp time: 0.00623213 5.15%
Mpole time: 0.0211822 17.50% Mpole time: 0.0210595 17.40%
Induce time: 0.0497719 41.12% Induce time: 0.0506279 41.83%
Polar time: 0.0274737 22.70% Polar time: 0.026832 22.17%
Qxfer time: 0.00294446 2.43% Qxfer time: 0.00292863 2.42%
Total time: 0.121048 Total time: 0.121027
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.12105 | 0.12112 | 0.12123 | 0.0 | 99.14 Pair | 0.12089 | 0.12109 | 0.12131 | 0.0 | 99.25
Bond | 5.27e-05 | 5.9124e-05 | 6.5605e-05 | 0.0 | 0.05 Bond | 4.8642e-05 | 5.2114e-05 | 6.0555e-05 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00038065 | 0.0005645 | 0.00066198 | 0.0 | 0.46 Comm | 0.00035781 | 0.00058015 | 0.00076608 | 0.0 | 0.48
Output | 0.00030705 | 0.00035011 | 0.00042646 | 0.0 | 0.29 Output | 0.0001878 | 0.00022879 | 0.00026441 | 0.0 | 0.19
Modify | 2.8994e-05 | 3.163e-05 | 3.6394e-05 | 0.0 | 0.03 Modify | 1.7668e-05 | 1.8481e-05 | 1.9751e-05 | 0.0 | 0.02
Other | | 4.464e-05 | | | 0.04 Other | | 3.389e-05 | | | 0.03
Nlocal: 162 ave 166 max 159 min Nlocal: 162 ave 166 max 159 min
Histogram: 2 0 0 0 0 0 0 1 0 1 Histogram: 2 0 0 0 0 0 0 1 0 1

31
examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.1
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@ -47,6 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key pair_coeff * * amoeba_water.prm amoeba_water.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -107,29 +108,29 @@ Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 Mbytes
3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354 3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354
4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932 4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932
5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205 5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205
Loop time of 0.000286908 on 1 procs for 5 steps with 6 atoms Loop time of 0.000214688 on 1 procs for 5 steps with 6 atoms
Performance: 1505.709 ns/day, 0.016 hours/ns, 17427.189 timesteps/s Performance: 2012.222 ns/day, 0.012 hours/ns, 23289.611 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads 65.7% CPU use with 1 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown: AMOEBA timing breakdown:
Init time: 7.417e-06 4.75% Init time: 5.306e-06 4.54%
Hal time: 8.458e-06 5.42% Hal time: 6.681e-06 5.72%
Mpole time: 2.2734e-05 14.57% Mpole time: 1.6221e-05 13.88%
Induce time: 7.4016e-05 47.43% Induce time: 5.6723e-05 48.54%
Polar time: 4.2972e-05 27.54% Polar time: 3.1532e-05 26.98%
Total time: 0.00015604 Total time: 0.000116854
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.00015922 | 0.00015922 | 0.00015922 | 0.0 | 55.49 Pair | 0.00011888 | 0.00011888 | 0.00011888 | 0.0 | 55.37
Bond | 5.034e-06 | 5.034e-06 | 5.034e-06 | 0.0 | 1.75 Bond | 3.797e-06 | 3.797e-06 | 3.797e-06 | 0.0 | 1.77
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.49e-07 | 8.49e-07 | 8.49e-07 | 0.0 | 0.30 Comm | 7.24e-07 | 7.24e-07 | 7.24e-07 | 0.0 | 0.34
Output | 0.00011336 | 0.00011336 | 0.00011336 | 0.0 | 39.51 Output | 8.4738e-05 | 8.4738e-05 | 8.4738e-05 | 0.0 | 39.47
Modify | 2.093e-06 | 2.093e-06 | 2.093e-06 | 0.0 | 0.73 Modify | 1.53e-06 | 1.53e-06 | 1.53e-06 | 0.0 | 0.71
Other | | 6.355e-06 | | | 2.21 Other | | 5.022e-06 | | | 2.34
Nlocal: 6 ave 6 max 6 min Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

31
examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.4
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@ -47,6 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key pair_coeff * * amoeba_water.prm amoeba_water.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -107,29 +108,29 @@ Per MPI rank memory allocation (min/avg/max) = 48.35 | 48.48 | 48.62 Mbytes
3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354 3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354
4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932 4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932
5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205 5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205
Loop time of 0.000582267 on 4 procs for 5 steps with 6 atoms Loop time of 0.000598353 on 4 procs for 5 steps with 6 atoms
Performance: 741.928 ns/day, 0.032 hours/ns, 8587.130 timesteps/s Performance: 721.982 ns/day, 0.033 hours/ns, 8356.278 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads 98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown: AMOEBA timing breakdown:
Init time: 1.3264e-05 3.71% Init time: 1.3678e-05 3.81%
Hal time: 3.16275e-06 0.88% Hal time: 3.5045e-06 0.97%
Mpole time: 2.35955e-05 6.60% Mpole time: 2.3748e-05 6.61%
Induce time: 0.000290896 81.33% Induce time: 0.000284514 79.15%
Polar time: 2.62723e-05 7.34% Polar time: 3.3521e-05 9.33%
Total time: 0.000357696 Total time: 0.000359445
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.00036015 | 0.00038587 | 0.00040555 | 0.0 | 66.27 Pair | 0.00035282 | 0.00038565 | 0.00040584 | 0.0 | 64.45
Bond | 1.441e-06 | 3.3365e-06 | 5.265e-06 | 0.0 | 0.57 Bond | 1.637e-06 | 3.2485e-06 | 4.816e-06 | 0.0 | 0.54
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.1512e-05 | 3.3761e-05 | 4.9368e-05 | 0.0 | 5.80 Comm | 1.4157e-05 | 3.2696e-05 | 5.1431e-05 | 0.0 | 5.46
Output | 0.00012269 | 0.00014666 | 0.00017989 | 0.0 | 25.19 Output | 0.00014589 | 0.0001627 | 0.00018978 | 0.0 | 27.19
Modify | 1.659e-06 | 2.0448e-06 | 2.275e-06 | 0.0 | 0.35 Modify | 1.649e-06 | 2.0097e-06 | 2.209e-06 | 0.0 | 0.34
Other | | 1.059e-05 | | | 1.82 Other | | 1.205e-05 | | | 2.01
Nlocal: 1.5 ave 3 max 0 min Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2 Histogram: 2 0 0 0 0 0 0 0 0 2

33
examples/amoeba/log.5Jul22.water_dimer.hippo.g++.1
View File

@ -47,6 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
pair_style hippo pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key pair_coeff * * hippo_water.prm hippo_water.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -109,31 +110,31 @@ Per MPI rank memory allocation (min/avg/max) = 47.9 | 47.9 | 47.9 Mbytes
3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978 3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978
4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156 4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156
5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154 5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154
Loop time of 0.000211279 on 1 procs for 5 steps with 6 atoms Loop time of 0.000210439 on 1 procs for 5 steps with 6 atoms
Performance: 2044.690 ns/day, 0.012 hours/ns, 23665.390 timesteps/s Performance: 2052.851 ns/day, 0.012 hours/ns, 23759.854 timesteps/s
98.4% CPU use with 1 MPI tasks x 1 OpenMP threads 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
HIPPO timing breakdown: HIPPO timing breakdown:
Init time: 4.768e-06 4.20% Init time: 5.006e-06 4.58%
Repulse time: 1.3408e-05 11.81% Repulse time: 1.3587e-05 12.42%
Disp time: 9.476e-06 8.35% Disp time: 5.471e-06 5.00%
Mpole time: 2.1547e-05 18.98% Mpole time: 2.1321e-05 19.49%
Induce time: 3.7631e-05 33.14% Induce time: 3.7665e-05 34.43%
Polar time: 2.4333e-05 21.43% Polar time: 2.3919e-05 21.87%
Qxfer time: 2.244e-06 1.98% Qxfer time: 2.295e-06 2.10%
Total time: 0.000113542 Total time: 0.000109391
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.00011535 | 0.00011535 | 0.00011535 | 0.0 | 54.60 Pair | 0.00011125 | 0.00011125 | 0.00011125 | 0.0 | 52.86
Bond | 3.239e-06 | 3.239e-06 | 3.239e-06 | 0.0 | 1.53 Bond | 3.062e-06 | 3.062e-06 | 3.062e-06 | 0.0 | 1.46
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.41e-07 | 6.41e-07 | 6.41e-07 | 0.0 | 0.30 Comm | 6.3e-07 | 6.3e-07 | 6.3e-07 | 0.0 | 0.30
Output | 8.5752e-05 | 8.5752e-05 | 8.5752e-05 | 0.0 | 40.59 Output | 8.8087e-05 | 8.8087e-05 | 8.8087e-05 | 0.0 | 41.86
Modify | 1.55e-06 | 1.55e-06 | 1.55e-06 | 0.0 | 0.73 Modify | 1.664e-06 | 1.664e-06 | 1.664e-06 | 0.0 | 0.79
Other | | 4.744e-06 | | | 2.25 Other | | 5.749e-06 | | | 2.73
Nlocal: 6 ave 6 max 6 min Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

35
examples/amoeba/log.5Jul22.water_dimer.hippo.g++.4
View File

@ -47,6 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
pair_style hippo pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key pair_coeff * * hippo_water.prm hippo_water.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -109,31 +110,31 @@ Per MPI rank memory allocation (min/avg/max) = 47.91 | 48.04 | 48.18 Mbytes
3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978 3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978
4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156 4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156
5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154 5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154
Loop time of 0.000515971 on 4 procs for 5 steps with 6 atoms Loop time of 0.000488464 on 4 procs for 5 steps with 6 atoms
Performance: 837.257 ns/day, 0.029 hours/ns, 9690.472 timesteps/s Performance: 884.405 ns/day, 0.027 hours/ns, 10236.169 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads 70.9% CPU use with 4 MPI tasks x 1 OpenMP threads
HIPPO timing breakdown: HIPPO timing breakdown:
Init time: 1.26765e-05 4.09% Init time: 1.2924e-05 4.50%
Repulse time: 1.99082e-05 6.43% Repulse time: 2.01283e-05 7.01%
Disp time: 3.16825e-06 1.02% Disp time: 3.04475e-06 1.06%
Mpole time: 3.4956e-05 11.29% Mpole time: 3.51807e-05 12.25%
Induce time: 0.000205268 66.29% Induce time: 0.000183034 63.71%
Polar time: 3.1924e-05 10.31% Polar time: 3.13832e-05 10.92%
Qxfer time: 1.5545e-06 0.50% Qxfer time: 1.44475e-06 0.50%
Total time: 0.000309632 Total time: 0.000287298
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.0003033 | 0.00032943 | 0.00034747 | 0.0 | 63.85 Pair | 0.00028193 | 0.00030553 | 0.00032173 | 0.0 | 62.55
Bond | 1.237e-06 | 2.778e-06 | 4.775e-06 | 0.0 | 0.54 Bond | 1.317e-06 | 2.7712e-06 | 4.847e-06 | 0.0 | 0.57
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.2356e-05 | 3.1848e-05 | 4.3553e-05 | 0.0 | 6.17 Comm | 1.3015e-05 | 3.0698e-05 | 4.1342e-05 | 0.0 | 6.28
Output | 0.00012443 | 0.0001412 | 0.00015698 | 0.0 | 27.37 Output | 0.00012315 | 0.00013964 | 0.00015356 | 0.0 | 28.59
Modify | 1.428e-06 | 2.0447e-06 | 2.545e-06 | 0.0 | 0.40 Modify | 1.445e-06 | 1.881e-06 | 2.366e-06 | 0.0 | 0.39
Other | | 8.678e-06 | | | 1.68 Other | | 7.949e-06 | | | 1.63
Nlocal: 1.5 ave 3 max 0 min Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2 Histogram: 2 0 0 0 0 0 0 0 0 2

29
examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.1
View File

@ -47,6 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key pair_coeff * * amoeba_water.prm amoeba_water.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -106,29 +107,29 @@ Per MPI rank memory allocation (min/avg/max) = 48.28 | 48.28 | 48.28 Mbytes
3 15.996484 -46.59119 0.087228651 1.3862662 0 0 1.4734948 -44.307093 15705.166 28374.161 4124.662 13087.621 -6242.1769 3159.6508 1787.4159 3 15.996484 -46.59119 0.087228651 1.3862662 0 0 1.4734948 -44.307093 15705.166 28374.161 4124.662 13087.621 -6242.1769 3159.6508 1787.4159
4 10.888785 -45.839064 0.062461924 0.96598997 0 0 1.0284519 -44.258837 30226.38 48920.372 15666.108 25051.837 -9443.9251 2603.8275 435.5257 4 10.888785 -45.839064 0.062461924 0.96598997 0 0 1.0284519 -44.258837 30226.38 48920.372 15666.108 25051.837 -9443.9251 2603.8275 435.5257
5 10.58575 -45.503287 0.071817565 0.64254674 0 0 0.71436431 -44.252503 31899.04 51066.283 18170.57 25448.409 -9478.6752 638.72265 -1011.7679 5 10.58575 -45.503287 0.071817565 0.64254674 0 0 0.71436431 -44.252503 31899.04 51066.283 18170.57 25448.409 -9478.6752 638.72265 -1011.7679
Loop time of 0.00100021 on 1 procs for 5 steps with 18 atoms Loop time of 0.00100127 on 1 procs for 5 steps with 18 atoms
Performance: 431.907 ns/day, 0.056 hours/ns, 4998.925 timesteps/s Performance: 431.450 ns/day, 0.056 hours/ns, 4993.633 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown: AMOEBA timing breakdown:
Init time: 1.2295e-05 1.38% Init time: 1.2944e-05 1.45%
Hal time: 6.2308e-05 6.98% Hal time: 6.4578e-05 7.21%
Mpole time: 0.000124591 13.97% Mpole time: 0.000124703 13.93%
Induce time: 0.000432719 48.51% Induce time: 0.000435232 48.60%
Polar time: 0.000259676 29.11% Polar time: 0.000257613 28.77%
Total time: 0.000892068 Total time: 0.000895454
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.00089392 | 0.00089392 | 0.00089392 | 0.0 | 89.37 Pair | 0.00089735 | 0.00089735 | 0.00089735 | 0.0 | 89.62
Bond | 6.685e-06 | 6.685e-06 | 6.685e-06 | 0.0 | 0.67 Bond | 6.783e-06 | 6.783e-06 | 6.783e-06 | 0.0 | 0.68
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.67e-07 | 6.67e-07 | 6.67e-07 | 0.0 | 0.07 Comm | 6.36e-07 | 6.36e-07 | 6.36e-07 | 0.0 | 0.06
Output | 9.0869e-05 | 9.0869e-05 | 9.0869e-05 | 0.0 | 9.08 Output | 8.9119e-05 | 8.9119e-05 | 8.9119e-05 | 0.0 | 8.90
Modify | 2.517e-06 | 2.517e-06 | 2.517e-06 | 0.0 | 0.25 Modify | 2.385e-06 | 2.385e-06 | 2.385e-06 | 0.0 | 0.24
Other | | 5.561e-06 | | | 0.56 Other | | 4.998e-06 | | | 0.50
Nlocal: 18 ave 18 max 18 min Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

31
examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.4
View File

@ -47,6 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ...
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key pair_coeff * * amoeba_water.prm amoeba_water.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -107,29 +108,29 @@ Per MPI rank memory allocation (min/avg/max) = 48.3 | 48.3 | 48.3 Mbytes
3 15.996484 -46.59119 0.087228651 1.3862662 0 0 1.4734948 -44.307093 15705.166 28374.161 4124.662 13087.621 -6242.1769 3159.6508 1787.4159 3 15.996484 -46.59119 0.087228651 1.3862662 0 0 1.4734948 -44.307093 15705.166 28374.161 4124.662 13087.621 -6242.1769 3159.6508 1787.4159
4 10.888785 -45.839064 0.062461924 0.96598997 0 0 1.0284519 -44.258837 30226.38 48920.372 15666.108 25051.837 -9443.9251 2603.8275 435.5257 4 10.888785 -45.839064 0.062461924 0.96598997 0 0 1.0284519 -44.258837 30226.38 48920.372 15666.108 25051.837 -9443.9251 2603.8275 435.5257
5 10.58575 -45.503287 0.071817565 0.64254674 0 0 0.71436431 -44.252503 31899.04 51066.283 18170.57 25448.409 -9478.6752 638.72265 -1011.7679 5 10.58575 -45.503287 0.071817565 0.64254674 0 0 0.71436431 -44.252503 31899.04 51066.283 18170.57 25448.409 -9478.6752 638.72265 -1011.7679
Loop time of 0.0015204 on 4 procs for 5 steps with 18 atoms Loop time of 0.00124102 on 4 procs for 5 steps with 18 atoms
Performance: 284.136 ns/day, 0.084 hours/ns, 3288.611 timesteps/s Performance: 348.100 ns/day, 0.069 hours/ns, 4028.938 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads 99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown: AMOEBA timing breakdown:
Init time: 2.00392e-05 1.57% Init time: 1.93587e-05 1.89%
Hal time: 2.58605e-05 2.02% Hal time: 2.20198e-05 2.15%
Mpole time: 0.000137192 10.74% Mpole time: 0.0001019 9.94%
Induce time: 0.000858714 67.22% Induce time: 0.000717017 69.95%
Polar time: 0.00023507 18.40% Polar time: 0.000164237 16.02%
Total time: 0.00127742 Total time: 0.00102505
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.0012876 | 0.0012913 | 0.0012951 | 0.0 | 84.93 Pair | 0.0010331 | 0.0010362 | 0.0010375 | 0.0 | 83.50
Bond | 4.076e-06 | 6.434e-06 | 1.0051e-05 | 0.0 | 0.42 Bond | 3.723e-06 | 5.0355e-06 | 5.6e-06 | 0.0 | 0.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.4924e-05 | 5.9337e-05 | 8.3417e-05 | 0.0 | 3.90 Comm | 1.7872e-05 | 4.1093e-05 | 6.4155e-05 | 0.0 | 3.31
Output | 0.00012796 | 0.00014846 | 0.00018928 | 0.0 | 9.76 Output | 0.00012756 | 0.00014764 | 0.00016933 | 0.0 | 11.90
Modify | 2.066e-06 | 2.5358e-06 | 3.07e-06 | 0.0 | 0.17 Modify | 1.808e-06 | 2.4647e-06 | 2.74e-06 | 0.0 | 0.20
Other | | 1.236e-05 | | | 0.81 Other | | 8.565e-06 | | | 0.69
Nlocal: 4.5 ave 6 max 3 min Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1 Histogram: 1 0 0 1 0 0 1 0 0 1

37
examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.1
View File

@ -41,12 +41,13 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000 seconds special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds read_data CPU = 0.003 seconds
# force field # force field
pair_style hippo pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key pair_coeff * * hippo_water.prm hippo_water.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -108,31 +109,31 @@ Per MPI rank memory allocation (min/avg/max) = 47.84 | 47.84 | 47.84 Mbytes
3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633 3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633
4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368 4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368
5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826 5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826
Loop time of 0.00117792 on 1 procs for 5 steps with 18 atoms Loop time of 0.000984386 on 1 procs for 5 steps with 18 atoms
Performance: 366.749 ns/day, 0.065 hours/ns, 4244.778 timesteps/s Performance: 438.852 ns/day, 0.055 hours/ns, 5079.308 timesteps/s
95.2% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
HIPPO timing breakdown: HIPPO timing breakdown:
Init time: 1.5876e-05 1.52% Init time: 1.2669e-05 1.45%
Repulse time: 0.000160405 15.32% Repulse time: 0.000132325 15.15%
Disp time: 5.1301e-05 4.90% Disp time: 4.2534e-05 4.87%
Mpole time: 0.000219996 21.01% Mpole time: 0.000177341 20.30%
Induce time: 0.000352821 33.70% Induce time: 0.000303723 34.77%
Polar time: 0.000218541 20.87% Polar time: 0.000179318 20.53%
Qxfer time: 2.7842e-05 2.66% Qxfer time: 2.5413e-05 2.91%
Total time: 0.00104695 Total time: 0.000873466
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.0010494 | 0.0010494 | 0.0010494 | 0.0 | 89.09 Pair | 0.00087559 | 0.00087559 | 0.00087559 | 0.0 | 88.95
Bond | 7.408e-06 | 7.408e-06 | 7.408e-06 | 0.0 | 0.63 Bond | 6.455e-06 | 6.455e-06 | 6.455e-06 | 0.0 | 0.66
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.032e-06 | 1.032e-06 | 1.032e-06 | 0.0 | 0.09 Comm | 7.87e-07 | 7.87e-07 | 7.87e-07 | 0.0 | 0.08
Output | 0.00011139 | 0.00011139 | 0.00011139 | 0.0 | 9.46 Output | 9.3142e-05 | 9.3142e-05 | 9.3142e-05 | 0.0 | 9.46
Modify | 2.647e-06 | 2.647e-06 | 2.647e-06 | 0.0 | 0.22 Modify | 2.351e-06 | 2.351e-06 | 2.351e-06 | 0.0 | 0.24
Other | | 6.086e-06 | | | 0.52 Other | | 6.065e-06 | | | 0.62
Nlocal: 18 ave 18 max 18 min Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

37
examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.4
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@ -41,12 +41,13 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.000 seconds special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds read_data CPU = 0.004 seconds
# force field # force field
pair_style hippo pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key pair_coeff * * hippo_water.prm hippo_water.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ... Finding 1-2 1-3 1-4 neighbors ...
@ -109,31 +110,31 @@ Per MPI rank memory allocation (min/avg/max) = 47.86 | 47.86 | 47.86 Mbytes
3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633 3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633
4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368 4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368
5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826 5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826
Loop time of 0.000850973 on 4 procs for 5 steps with 18 atoms Loop time of 0.00126451 on 4 procs for 5 steps with 18 atoms
Performance: 507.654 ns/day, 0.047 hours/ns, 5875.629 timesteps/s Performance: 341.634 ns/day, 0.070 hours/ns, 3954.096 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads 92.2% CPU use with 4 MPI tasks x 1 OpenMP threads
HIPPO timing breakdown: HIPPO timing breakdown:
Init time: 1.6627e-05 2.46% Init time: 1.75712e-05 1.72%
Repulse time: 9.88147e-05 14.60% Repulse time: 0.000116156 11.39%
Disp time: 1.35375e-05 2.00% Disp time: 1.69788e-05 1.66%
Mpole time: 0.000103418 15.28% Mpole time: 0.000178714 17.52%
Induce time: 0.000343719 50.80% Induce time: 0.000515806 50.57%
Polar time: 9.3749e-05 13.85% Polar time: 0.0001659 16.27%
Qxfer time: 6.64925e-06 0.98% Qxfer time: 8.64975e-06 0.85%
Total time: 0.000676665 Total time: 0.00101993
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.00068159 | 0.00068738 | 0.00069496 | 0.0 | 80.78 Pair | 0.0010223 | 0.0010316 | 0.001045 | 0.0 | 81.58
Bond | 3.506e-06 | 3.8025e-06 | 4.338e-06 | 0.0 | 0.45 Bond | 3.062e-06 | 4.3805e-06 | 5.123e-06 | 0.0 | 0.35
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.1451e-05 | 4.4141e-05 | 5.7694e-05 | 0.0 | 5.19 Comm | 1.4853e-05 | 6.5245e-05 | 9.2753e-05 | 0.0 | 5.16
Output | 9.6072e-05 | 0.00010517 | 0.00013106 | 0.0 | 12.36 Output | 0.0001294 | 0.00014959 | 0.00018927 | 0.0 | 11.83
Modify | 1.799e-06 | 1.9772e-06 | 2.149e-06 | 0.0 | 0.23 Modify | 1.595e-06 | 2.2495e-06 | 2.798e-06 | 0.0 | 0.18
Other | | 8.507e-06 | | | 1.00 Other | | 1.145e-05 | | | 0.91
Nlocal: 4.5 ave 6 max 3 min Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1 Histogram: 1 0 0 1 0 0 1 0 0 1